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1vk1

From Proteopedia

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[[Image:1vk1.jpg|left|200px]]<br /><applet load="1vk1" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1vk1, resolution 1.20&Aring;" />
 
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'''Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001'''<br />
 
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==About this Structure==
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==Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001==
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1VK1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=NA:'>NA</scene> and <scene name='pdbligand=PEG:'>PEG</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK1 OCA].
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<StructureSection load='1vk1' size='340' side='right'caption='[[1vk1]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
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[[Category: Pyrococcus furiosus]]
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== Structural highlights ==
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[[Category: Single protein]]
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<table><tr><td colspan='2'>[[1vk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VK1 FirstGlance]. <br>
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[[Category: Adams, M W.W.]]
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
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[[Category: Brereton, P S.]]
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLY:N-DIMETHYL-LYSINE'>MLY</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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[[Category: Chang, J C.]]
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1vk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk1 OCA], [https://pdbe.org/1vk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vk1 RCSB], [https://www.ebi.ac.uk/pdbsum/1vk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk1 ProSAT], [https://www.topsan.org/Proteins/SECSG/1vk1 TOPSAN]</span></td></tr>
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[[Category: Chen, L.]]
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</table>
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[[Category: II, F L.Poole.]]
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== Function ==
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[[Category: Izumi, M.]]
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[https://www.uniprot.org/uniprot/Q8U3S5_PYRFU Q8U3S5_PYRFU]
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[[Category: Jr., F E.Jenney.]]
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== Evolutionary Conservation ==
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[[Category: Lee, D.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Liu, Z J.]]
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Check<jmol>
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[[Category: Ng, J D.]]
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<jmolCheckbox>
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[[Category: Richardson, D C.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/1vk1_consurf.spt"</scriptWhenChecked>
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[[Category: Richardson, J S.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: Rose, J P.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: SECSG, Southeast Collaboratory for Structural Genomics.]]
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</jmolCheckbox>
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[[Category: Shah, A.]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1vk1 ConSurf].
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[[Category: Shah, C.]]
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<div style="clear:both"></div>
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[[Category: Sugar, F J.]]
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<div style="background-color:#fffaf0;">
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[[Category: Tempel, W.]]
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== Publication Abstract from PubMed ==
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[[Category: Wang, B C.]]
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BACKGROUND: The major bottleneck for determination of 3 D structures of proteins using X-rays is the production of diffraction quality crystals. Often proteins are subjected to chemical modification to improve the chances of crystallization RESULTS: Here, we report the successful crystallization of a nuclease employing a reductive methylation protocol. The key to crystallization was the successful introduction of 44 new cohesive (NZ) CH...O contacts (3.2-3.7 A) by the addition of 2 methyl groups to the side chain amine nitrogen (NZ) of 9 lysine residues of the nuclease. The new contacts dramatically altered the crystallization properties of the protein, resulting in crystals that diffracted to 1.2 A resolution. Analytical ultracentrifugation analysis and thermodynamics results revealed a more compact protein structure with better solvent exclusion of buried Trp residues in the folded state of the methylated protein, assisting crystallization. CONCLUSION: In this study, introduction of novel cohesive (NZ)CH...O contacts by reductive methylation resulted in the crystallization of a protein that had previously resisted crystallization in spite of extensive purification and crystallization space screening. Introduction of (NZ)CH...O contacts could provide a solution to crystallization problems for a broad range of protein targets.
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[[Category: Yang, H.]]
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[[Category: Zhao, M.]]
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[[Category: NA]]
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[[Category: PEG]]
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[[Category: PO4]]
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[[Category: conserved hypothetical protein]]
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[[Category: dimethyl lysine]]
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[[Category: protein structure initiative]]
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[[Category: psi]]
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[[Category: pyrococcus furiosus]]
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[[Category: reductive methylation]]
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[[Category: secsg]]
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[[Category: southeast collaboratory for structural genomics]]
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[[Category: structural genomics]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:36:06 2008''
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(NZ)CH...O contacts assist crystallization of a ParB-like nuclease.,Shaw N, Cheng C, Tempel W, Chang J, Ng J, Wang XY, Perrett S, Rose J, Rao Z, Wang BC, Liu ZJ BMC Struct Biol. 2007 Jul 7;7:46. PMID:17617922<ref>PMID:17617922</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1vk1" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Pyrococcus furiosus]]
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[[Category: Adams MWW]]
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[[Category: Brereton PS]]
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[[Category: Chang J]]
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[[Category: Chen L]]
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[[Category: Izumi M]]
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[[Category: Jenney Jr FE]]
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[[Category: Lee D]]
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[[Category: Liu ZJ]]
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[[Category: Ng J]]
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[[Category: Poole II FL]]
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[[Category: Richardson DC]]
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[[Category: Richardson JS]]
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[[Category: Rose J]]
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[[Category: Shah A]]
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[[Category: Shah C]]
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[[Category: Sugar FJ]]
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[[Category: Tempel W]]
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[[Category: Wang BC]]
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[[Category: Yang H]]
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[[Category: Zhao M]]

Current revision

Conserved hypothetical protein from Pyrococcus furiosus Pfu-392566-001

PDB ID 1vk1

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